Prerequisites

Must have taken at least one of the following
courses at Davidson: Genetics, Microbiology, Immunology, Genomics, Development,
Biochemistry, or Bioinformatics. If you have not taken these biology courses
(e.g., your are a younger Biology major, Chemistry, Math, or Physics majors,
etc.) and are still interested, you can seek permission from the instructor.

GradingGrades will be based on lead presentations
(30%), supporting roles (15%), skeptic roles (15%), wiki site (10% - group
grade), term paper (20%), and speaker visit (10%). Assignments turned in
late will be docked 1 letter grade for each 24 hour period.

Logistical DetailsCeiling will be capped at 12 students. Order of student presentations
will be organized the first day of class, as will assignments for inviting
a speaker and producing a Synthetic Biology web site. Instructor will lead
the first session with students serving in other roles.

Honor Code
Work presented by you (in oral or written format) is to be original work produced
by you. It is considered an Honor
Code violation if someone takes credit for work he or she
does not deserve. Clearly, you will rely heavily on the written work of
others, but you need to balance the number and amount of direct quotes
with a synthesis of their work written in your own words. You should consult
the Biology
Department's plagiarism web site for additional help.

Fourier Analysis: "In signal processing and related
fields, Fourier analysis is typically thought of as decomposing a signal
into its component frequencies and their amplitudes." (from
Wikipedia)

Hysteretic behavior: "Hysteresis is a property of systems (usually physical
systems) that do not instantly follow the forces applied to them, but react
slowly, or do not return completely to their original state: that is, systems
whose states depend on their immediate history. For instance, if you push
on a piece of putty it will assume a new shape, and when you remove your
hand it will not return to its original shape, or at least not immediately
and not entirely. The term derives from an ancient Greek word υστ?ρησις,
meaning 'deficiency'. The term was coined by Sir James Alfred Ewing." (
from The Free Dictionary)

stochastic vs. chaotic: "Stochastic, from
the Greek "stochos" or "aim,
guess", means of, relating to, or characterized by conjecture and
randomness. A stochastic process is one whose behavior is non-deterministic
in that a state does not fully determine its next state." (from
Wikipedia)
"In mathematics and physics, chaos theory describes the behavior
of certain nonlinear dynamical systems that under specific conditions exhibit
dynamics that are sensitive to initial conditions (popularly referred to
as the butterfly
effect). As a result of this sensitivity, the behavior of chaotic systems
appears to be random, because of an exponential growth of errors in the initial
conditions. This happens even though these systems are deterministic in the
sense that their future dynamics are well defined by their initial conditions,
and with no random elements involved. This behavior is known as deterministic
chaos, or simply chaos.The butterfly effect is a phrase that encapsulates
the more technical notion of sensitive dependence on initial conditions in
chaos theory. Small variations of the initial condition of a nonlinear dynamical
system may produce large variations in the long term behavior of the system.
So this is sometimes presented as esoteric behavior, but can be exhibited
by very simple systems: for example, a ball placed at the crest of a hill
might roll into any of several valleys depending on slight differences in
initial position.
The phrase refers to the idea that a butterfly's wings might create tiny
changes in the atmosphere that ultimately cause a tornado to appear (or prevent
a tornado from appearing). The flapping wing represents a small change in
the initial condition of the system, which causes a chain of events leading
to large-scale phenomena. Had the butterfly not flapped its wings, the trajectory
of the system might have been vastly different." (from
Wikipedia)

Competing Financial Interests Declaration: J.D.K. is a founder of Amyris
Biotechnologies, a company that may eventually use the genes and yeast
strains described in this paper for the production of artemisinin. However,
neither Amyris Biotechnologies nor the University of California will make
any profit from the production and sale of the antimalarial drug artemisinin.

Transposons: transposons are
sequences of DNA that can move around to different positions within the
genome of a single cell, a process called transposition. In the process,
they can cause mutations and change the amount of DNA in the genome. Transposons
are also called "jumping
genes", and are examples of mobile genetic elements. Discovered
by Barbara McClintock early in her career[1], the topic went on to be
a Nobel prize winning work in 1983. There are a variety of mobile genetic
elements, and they can be grouped based on their mechanism of transposition.
Class I mobile genetic elements, or retrotransposons, move in the genome
by being transcribed to RNA and then back to DNA by reverse transcriptase,
while class II mobile genetic elements move directly from one position
to another within the genome using a transposase to "cut and paste" them
within the genome. Transposons are very useful to researchers as a means
to alter DNA inside of a living organism. Transposons make up a large
fraction of genome sizes which is evident through the C-values of eukaryotic
species. (wikipedia)

Directed evolution is a method used in protein engineering to harness the
power of Darwinian selection to evolve proteins or RNA with desirable properties
not found in nature. A typical directed evolution experiment involves three
steps:

Diversification: The gene encoding the protein of interest is mutated
and/or recombined at random to create a large library of gene
variants. Techniques commonly used in this step are error-prone PCR and
DNA shuffling.

Selection: The library is tested for the presence of mutants (variants)
possessing the desired property using a screen or selection.
Screens enable the researcher to identify and isolate high-performing
mutants by hand, while selections automatically eliminate all nonfunctional
mutants.

Amplification:
The variants identified in the selection or screen are replicated
manyfold, enabling researchers to sequence their DNA in order to understand
what mutations have occurred.

Together, these three steps are termed a "round" of directed
evolution. Most experiments will perform more than one round. In
these experiments, the "winners" of the previous round are diversified
in the next round to create a new library. At the end of the experiment,
all evolved protein or RNA mutants are characterized using biochemical
methods. (wikipedia)

Supporting Figure 5
Fig. 5. The functional promoter library was analyzed by using flow cytometry.
The relative average geometric mean fluorescence of the members of the
library is illustrated above and exhibited a nearly 3-log fold range
after 14 h in a minimal media with 0.1% casamino acids.

Supporting Figure 6
Fig. 6. Above are representative light-field (right) and false-color dark-field
(Left) photomicrographs of clones with highly heterogeneous expression
of GFP. These promoters were not further analyzed and are not included
in the functional promoter library.

Supporting Figure 7
Fig. 7. In contrast, representative clones chosen for further analysis
had much more homogenous distributions of fluorescence. Below, two representative
sets of photomicrographs are shown. The top two images correspond to
a promoter with a relative promoter strength metric of 0.124 and the
bottom two to 0.417.